Journal articles

Machine learning techniques to characterize functional traits of plankton from image data

Eric C Orenstein ¹ Sakina-Dorothée Ayata ^{1, *} Frédéric Maps ² Érica C Becker ³ Fabio Benedetti ⁴ Tristan Biard ⁵ Thibault de Garidel-Thoron ⁶ Jeffrey S Ellen ⁷ Filippo Ferrario ² Sarah L C Giering ⁸ Tamar Guy-Haim ⁹ Laura Hoebeke ¹⁰ Morten Hvitfeldt Iversen ¹¹ Thomas Kiørboe ¹² Jean-François Lalonde ¹³ Arancha Lana ¹⁴ Martin Laviale ¹⁵ Fabien Lombard ^{1, 16} Tom Lorimer ¹⁷ Severine Martini ¹⁸ Albin Meyer ¹⁵ Klas Ove Möller ¹⁹ Barbara Niehoff ¹¹ Mark D Ohman ⁷ Cedric Pradalier ²⁰ Jean-Baptiste Romagnan ²¹ Simon-Martin Schröder ²² Virginie Sonnet ²³ Heidi M Sosik ²⁴ Lars S Stemmann ¹ Michiel Stock ¹⁰ Tuba Terbiyik-Kurt ²⁵ Nerea Valcárcel-Pérez ²⁶ Laure Vilgrain ¹ Guillaume Wacquet ²⁷ Anya M Waite ²⁸ Jean-Olivier Irisson ¹

* Corresponding author

1 LOV - Laboratoire d'océanographie de Villefranche

2 ULaval - Université Laval [Québec]

3 UFSC - Universidade Federal de Santa Catarina = Federal University of Santa Catarina [Florianópolis]

4 IBP - Institute of Biogeochemistry and Pollutant Dynamics [ETH Zürich]

5 LOG - Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187

6 CEREGE - Centre européen de recherche et d'enseignement des géosciences de l'environnement

7 SIO - Scripps Institution of Oceanography

8 NOC - National Oceanography Centre [Southampton]

9 Israel Oceanographic and Limnological Research - IOLR (ISRAEL)

10 UGENT - Universiteit Gent = Ghent University [Belgium]

11 AWI - Alfred Wegener Institute for Polar and Marine Research

12 DTU Centre for Ocean Life

13 LVSN - Laboratoire de Vision et Systèmes Numériques

14 IMEDEA - Institut Mediterrani d'Estudis Avancats

15 LIEC - Laboratoire Interdisciplinaire des Environnements Continentaux

16 IUF - Institut Universitaire de France

17 EAWAG - Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf]

18 MIO - Institut méditerranéen d'océanologie

19 Helmholtz-Zentrum Hereon

20 Georgia Tech Lorraine [Metz]

21 EMH - Écologie et Modèles pour l'Halieutique

22 Kiel University

23 URI - University of Rhode Island

24 WHOI - Woods Hole Oceanographic Institution

25 Cukurova University

26 Instituto Español de Oceanografía (IEO), Málaga.

27 IFREMER - Institut Français de Recherche pour l'Exploitation de la Mer

28 Dalhousie University [Halifax]

Abstract : Plankton imaging systems supported by automated classification and analysis have improved ecologists' ability to observe aquatic ecosystems. Today, we are on the cusp of reliably tracking plankton populations with a suite of lab-based and in situ tools, collecting imaging data at unprecedentedly fine spatial and temporal scales. But these data streams have potential well beyond examining the abundances of different taxa; the individual images themselves contain a wealth of information on functional traits. Here we outline traits that could be measured from image data, suggest computer vision approaches to extract functional trait information from the images, and discuss promising avenues for novel studies. The approaches we discuss are data agnostic and are broadly applicable to other aquatic or terrestrial organisms.

Keywords : Functional trait-based ecology plankton imaging machine learning

Document type :

Journal articles

Domain :

Life Sciences [q-bio] / Ecology, environment

Environmental Sciences / Biodiversity and Ecology

Complete list of metadata

https://hal.univ-lorraine.fr/hal-03482282
Contributor : Martin Laviale Connect in order to contact the contributor
Submitted on : Thursday, June 30, 2022 - 8:18:45 PM
Last modification on : Friday, August 5, 2022 - 12:36:12 PM

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Limnology Oceanography - 2022 ...

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